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<a href="particle__dynamics__diffusion__reaction_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;</div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="preprocessor">#ifndef PARTICLE_DYNAMICS_DIFFUSION_REACTION_HPP</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="preprocessor">#define PARTICLE_DYNAMICS_DIFFUSION_REACTION_HPP</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;</div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="particle__dynamics__diffusion__reaction_8h.html">particle_dynamics_diffusion_reaction.h</a>&quot;</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;</div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;{</div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;    DiffusionReactionInitialCondition&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;        DiffusionReactionInitialCondition(BodyType &amp;body)</div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;        : ParticleDynamicsSimple(body),</div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;          DiffusionReactionSimpleData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body),</div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;          pos_(this-&gt;particles_-&gt;pos_), species_n_(this-&gt;particles_-&gt;species_n_) {}</div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;    GetDiffusionTimeStepSize&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;        GetDiffusionTimeStepSize(BodyType &amp;body)</div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;        : ParticleDynamics&lt;Real&gt;(body),</div><div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;          DiffusionReactionSimpleData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body)</div><div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;    {</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;        Real smoothing_length = body.sph_adaptation_-&gt;ReferenceSmoothingLength();</div><div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;        diff_time_step_ = this-&gt;material_-&gt;getDiffusionTimeStepSize(smoothing_length);</div><div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;    }</div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;    RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;        RelaxationOfAllDiffusionSpeciesInner(BaseBodyRelationInner &amp;inner_relation)</div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;        : InteractionDynamicsWithUpdate(*inner_relation.sph_body_),</div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;          DiffusionReactionInnerData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(inner_relation),</div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;          species_n_(this-&gt;particles_-&gt;species_n_),</div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;          diffusion_dt_(this-&gt;particles_-&gt;diffusion_dt_), Vol_(this-&gt;particles_-&gt;Vol_)</div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    {</div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;        species_diffusion_ = this-&gt;material_-&gt;SpeciesDiffusion();</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    }</div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;        initializeDiffusionChangeRate(<span class="keywordtype">size_t</span> particle_i)</div><div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    {</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;        {</div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;            diffusion_dt_[m][particle_i] = 0;</div><div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;        }</div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;    }</div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;        getDiffusionChangeRate(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, <a class="code" href="class_vecd.html">Vecd</a> &amp;e_ij, Real surface_area_ij)</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    {</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;        {</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;            Real diff_coff_ij = species_diffusion_[m]-&gt;getInterParticleDiffusionCoff(particle_i, particle_j, e_ij);</div><div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;            <span class="keywordtype">size_t</span> l = species_diffusion_[m]-&gt;gradient_species_index_;</div><div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;            Real phi_ij = species_n_[l][particle_i] - species_n_[l][particle_j];</div><div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;            diffusion_dt_[m][particle_i] += diff_coff_ij * phi_ij * surface_area_ij;</div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;        }</div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    }</div><div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;        updateSpeciesDiffusion(<span class="keywordtype">size_t</span> particle_i, Real dt)</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    {</div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;        {</div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;            <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;            species_n_[k][particle_i] += dt * diffusion_dt_[m][particle_i];</div><div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;        }</div><div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    }</div><div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;        Interaction(<span class="keywordtype">size_t</span> index_i, Real dt)</div><div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    {</div><div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType&gt; *particles = this-&gt;particles_;</div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;        Neighborhood &amp;inner_neighborhood = this-&gt;inner_configuration_[index_i];</div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;</div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;        initializeDiffusionChangeRate(index_i);</div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> n = 0; n != inner_neighborhood.current_size_; ++n)</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;        {</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;            <span class="keywordtype">size_t</span> index_j = inner_neighborhood.j_[n];</div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;            Real dW_ij_ = inner_neighborhood.dW_ij_[n];</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;            Real r_ij_ = inner_neighborhood.r_ij_[n];</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;            <a class="code" href="class_vecd.html">Vecd</a> &amp;e_ij = inner_neighborhood.e_ij_[n];</div><div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div><div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;            <span class="keyword">const</span> <a class="code" href="class_vecd.html">Vecd</a> &amp;grad_ij = particles-&gt;getKernelGradient(index_i, index_j, dW_ij_, e_ij);</div><div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;            Real area_ij = 2.0 * Vol_[index_j] * dot(grad_ij, e_ij) / r_ij_;</div><div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;            getDiffusionChangeRate(index_i, index_j, e_ij, area_ij);</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;        }</div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    }</div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        Update(<span class="keywordtype">size_t</span> index_i, Real dt)</div><div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    {</div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;        updateSpeciesDiffusion(index_i, dt);</div><div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    }</div><div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;              <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    RelaxationOfAllDiffusionSpeciesComplex&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;                                            ContactBodyType, ContactBaseParticlesType, ContactBaseMaterialType&gt;::</div><div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        RelaxationOfAllDiffusionSpeciesComplex(ComplexBodyRelation &amp;complex_relation)</div><div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        : RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(complex_relation.inner_relation_),</div><div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;          DiffusionReactionContactData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;                                       ContactBodyType, ContactBaseParticlesType, ContactBaseMaterialType&gt;(complex_relation.contact_relation_),</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;          species_n_(this-&gt;particles_-&gt;species_n_), diffusion_dt_(this-&gt;particles_-&gt;diffusion_dt_)</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;    {</div><div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;        species_diffusion_ = this-&gt;material_-&gt;SpeciesDiffusion();</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;</div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k != this-&gt;contact_particles_.size(); ++k)</div><div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        {</div><div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;            contact_Vol_.push_back(&amp;(this-&gt;contact_particles_[k]-&gt;Vol_));</div><div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;            contact_species_n_.push_back(&amp;(this-&gt;contact_particles_[k]-&gt;species_n_));</div><div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;        }</div><div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;    }</div><div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;              <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div><div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesComplex&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;                                                 ContactBodyType, ContactBaseParticlesType, ContactBaseMaterialType&gt;::</div><div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;        getDiffusionChangeRateContact(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, <a class="code" href="class_vecd.html">Vecd</a> &amp;e_ij,</div><div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;                                      Real surface_area_ij, <span class="keyword">const</span> StdVec&lt;<a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a>&gt; &amp;species_n_k)</div><div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;    {</div><div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;        {</div><div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;            Real diff_coff_ij = species_diffusion_[m]-&gt;getInterParticleDiffusionCoff(particle_i, particle_j, e_ij);</div><div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;            <span class="keywordtype">size_t</span> l = species_diffusion_[m]-&gt;gradient_species_index_;</div><div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;            Real phi_ij = species_n_[l][particle_i] - species_n_k[l][particle_j];</div><div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;            diffusion_dt_[m][particle_i] += diff_coff_ij * phi_ij * surface_area_ij;</div><div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        }</div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;    }</div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;              <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div><div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllDiffusionSpeciesComplex&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;                                                 ContactBodyType, ContactBaseParticlesType, ContactBaseMaterialType&gt;::</div><div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        Interaction(<span class="keywordtype">size_t</span> index_i, Real dt)</div><div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;    {</div><div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;        RelaxationOfAllDiffusionSpeciesInner&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::Interaction(index_i, dt);</div><div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;        DiffusionReactionParticles&lt;BaseParticlesType&gt; *particles = this-&gt;particles_;</div><div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div><div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> k = 0; k &lt; this-&gt;contact_configuration_.size(); ++k)</div><div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        {</div><div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;            <a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a> &amp;Vol_k = *(contact_Vol_[k]);</div><div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;            StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_k = *(contact_species_n_[k]);</div><div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;</div><div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;            Neighborhood &amp;contact_neighborhood = (*this-&gt;contact_configuration_[k])[index_i];</div><div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> n = 0; n != contact_neighborhood.current_size_; ++n)</div><div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;            {</div><div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;                <span class="keywordtype">size_t</span> index_j = contact_neighborhood.j_[n];</div><div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;                Real r_ij_ = contact_neighborhood.r_ij_[n];</div><div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;                Real dW_ij_ = contact_neighborhood.dW_ij_[n];</div><div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;                <a class="code" href="class_vecd.html">Vecd</a> &amp;e_ij = contact_neighborhood.e_ij_[n];</div><div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;</div><div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;                <span class="keyword">const</span> <a class="code" href="class_vecd.html">Vecd</a> &amp;grad_ij = particles-&gt;getKernelGradient(index_i, index_j, dW_ij_, e_ij);</div><div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;                Real area_ij = 2.0 * Vol_k[index_j] * dot(grad_ij, e_ij) / r_ij_;</div><div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;                getDiffusionChangeRateContact(index_i, index_j, e_ij, area_ij, species_n_k);</div><div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;            }</div><div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;        }</div><div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;    }</div><div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;    InitializationRK&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        InitializationRK(SPHBody &amp;sph_body, StdVec&lt;<a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a>&gt; &amp;species_s)</div><div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;        : ParticleDynamicsSimple(sph_body),</div><div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;          DiffusionReactionSimpleData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(sph_body),</div><div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;          species_n_(this-&gt;particles_-&gt;species_n_), species_s_(species_s)</div><div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;    {</div><div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;        species_diffusion_ = this-&gt;material_-&gt;SpeciesDiffusion();</div><div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;    }</div><div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;    <span class="keywordtype">void</span> InitializationRK&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;        initializeIntermediateValue(<span class="keywordtype">size_t</span> particle_i)</div><div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;    {</div><div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; species_diffusion_.size(); ++m)</div><div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;        {</div><div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;            <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;            species_s_[m][particle_i] = species_n_[k][particle_i];</div><div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        }</div><div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;    }</div><div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;    <span class="keywordtype">void</span> InitializationRK&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;        Update(<span class="keywordtype">size_t</span> index_i, Real dt)</div><div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;    {</div><div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;        initializeIntermediateValue(index_i);</div><div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;    }</div><div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;    SecondStageRK2&lt;FirstStageType&gt;::</div><div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;        SecondStageRK2(<span class="keyword">typename</span> FirstStageType::BodyRelationType &amp;body_relation,</div><div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;                       StdVec&lt;<a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a>&gt; &amp;species_s)</div><div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;        : <a class="code" href="class_s_p_h_1_1_first_stage_type.html">FirstStageType</a>(body_relation),</div><div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;          species_n_(this-&gt;particles_-&gt;species_n_), diffusion_dt_(this-&gt;particles_-&gt;diffusion_dt_),</div><div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;          species_s_(species_s)</div><div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    {</div><div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;        species_diffusion_ = this-&gt;material_-&gt;SpeciesDiffusion();</div><div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    }</div><div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;    <span class="keywordtype">void</span> SecondStageRK2&lt;FirstStageType&gt;::</div><div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;        updateSpeciesDiffusion(<span class="keywordtype">size_t</span> particle_i, Real dt)</div><div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;    {</div><div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; this-&gt;species_diffusion_.size(); ++m)</div><div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;        {</div><div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;            <span class="keywordtype">size_t</span> k = species_diffusion_[m]-&gt;diffusion_species_index_;</div><div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;            species_n_[k][particle_i] = 0.5 * species_s_[m][particle_i] +</div><div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;                                        0.5 * (species_n_[k][particle_i] + dt * diffusion_dt_[m][particle_i]);</div><div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;        }</div><div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;    }</div><div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;    RelaxationOfAllDiffusionSpeciesRK2&lt;FirstStageType&gt;::</div><div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;        RelaxationOfAllDiffusionSpeciesRK2(<span class="keyword">typename</span> FirstStageType::BodyRelationType &amp;body_relation)</div><div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;        : ParticleDynamics&lt;void&gt;(*body_relation.sph_body_),</div><div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;          rk2_initialization_(*body_relation.sph_body_, species_s_),</div><div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;          rk2_1st_stage_(body_relation),</div><div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;          rk2_2nd_stage_(body_relation, species_s_)</div><div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;    {</div><div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;        StdVec&lt;BaseDiffusion *&gt; species_diffusion_ = rk2_1st_stage_.getMaterial()-&gt;SpeciesDiffusion();</div><div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;</div><div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;        <span class="keywordtype">size_t</span> number_of_diffusion_species = species_diffusion_.size();</div><div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;        species_s_.resize(number_of_diffusion_species);</div><div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; number_of_diffusion_species; ++m)</div><div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;        {</div><div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;            <span class="comment">// the size should be the same as that in the base particles</span></div><div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;            species_s_[m].resize(rk2_1st_stage_.getParticles()-&gt;real_particles_bound_);</div><div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;            <span class="comment">// register data in base particles</span></div><div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;            std::get&lt;0&gt;(rk2_1st_stage_.getParticles()-&gt;all_particle_data_).push_back(&amp;species_s_[m]);</div><div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;        }</div><div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;    }</div><div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ad1f02306798f50c9cbce664ea7c02105">  241</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ad1f02306798f50c9cbce664ea7c02105">RelaxationOfAllDiffusionSpeciesRK2&lt;FirstStageType&gt;::exec</a>(Real dt)</div><div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;    {</div><div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;        rk2_initialization_.exec();</div><div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;        rk2_1st_stage_.exec(dt);</div><div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;        rk2_2nd_stage_.exec(dt);</div><div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;    }</div><div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;    <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2&lt;FirstStageType&gt;::parallel_exec</a>(Real dt)</div><div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;    {</div><div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;        rk2_initialization_.parallel_exec();</div><div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;        rk2_1st_stage_.parallel_exec(dt);</div><div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;        rk2_2nd_stage_.parallel_exec(dt);</div><div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;    }</div><div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;    RelaxationOfAllReactionsForward&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;        RelaxationOfAllReactionsForward(BodyType &amp;body)</div><div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;        : ParticleDynamicsSimple(body),</div><div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;          DiffusionReactionSimpleData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body),</div><div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;          species_n_(this-&gt;particles_-&gt;species_n_)</div><div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;    {</div><div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;        species_reaction_ = this-&gt;material_-&gt;SpeciesReaction();</div><div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;    }</div><div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllReactionsForward&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;        Update(<span class="keywordtype">size_t</span> index_i, Real dt)</div><div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;    {</div><div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;        <a class="code" href="class_index_vector.html">IndexVector</a> &amp;reactive_species = species_reaction_-&gt;reactive_species_;</div><div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;</div><div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m != reactive_species.size(); ++m)</div><div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;        {</div><div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;            <span class="keywordtype">size_t</span> k = reactive_species[m];</div><div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;            Real production_rate = species_reaction_-&gt;get_production_rates_[k](species_n_, index_i);</div><div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;            Real loss_rate = species_reaction_-&gt;get_loss_rates_[k](species_n_, index_i);</div><div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;            species_n_[k][index_i] = updateAReactionSpecies(species_n_[k][index_i], production_rate, loss_rate, dt);</div><div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;        }</div><div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;    }</div><div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;    RelaxationOfAllReactionsBackward&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;        RelaxationOfAllReactionsBackward(BodyType &amp;body)</div><div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;        : ParticleDynamicsSimple(body),</div><div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;          DiffusionReactionSimpleData&lt;BodyType, <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>&gt;(body),</div><div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;          species_n_(this-&gt;particles_-&gt;species_n_)</div><div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;    {</div><div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;        species_reaction_ = this-&gt;material_-&gt;SpeciesReaction();</div><div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;    }</div><div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;    <span class="keywordtype">void</span> RelaxationOfAllReactionsBackward&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;::</div><div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;        Update(<span class="keywordtype">size_t</span> index_i, Real dt)</div><div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;    {</div><div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;        <a class="code" href="class_index_vector.html">IndexVector</a> &amp;reactive_species = species_reaction_-&gt;reactive_species_;</div><div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;</div><div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;        <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = reactive_species.size(); m != 0; --m)</div><div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;        {</div><div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;            <span class="keywordtype">size_t</span> k = reactive_species[m - 1];</div><div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;            Real production_rate = species_reaction_-&gt;get_production_rates_[k](species_n_, index_i);</div><div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;            Real loss_rate = species_reaction_-&gt;get_loss_rates_[k](species_n_, index_i);</div><div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;            species_n_[k][index_i] = updateAReactionSpecies(species_n_[k][index_i], production_rate, loss_rate, dt);</div><div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;        }</div><div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;    }</div><div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;    <span class="comment">//=================================================================================================//</span></div><div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;}</div><div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;<span class="preprocessor">#endif // PARTICLE_DYNAMICS_DIFFUSION_REACTION_HPP</span></div><div class="ttc" id="class_std_large_vec_3_01_real_01_4_html"><div class="ttname"><a href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt; Real &gt;</a></div></div>
<div class="ttc" id="class_index_vector_html"><div class="ttname"><a href="class_index_vector.html">IndexVector</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">SPH::RelaxationOfAllDiffusionSpeciesRK2</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species with second order Runge-Kutta time stepping...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:204</div></div>
<div class="ttc" id="class_s_p_h_1_1_first_stage_type_html"><div class="ttname"><a href="class_s_p_h_1_1_first_stage_type.html">FirstStageType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_base_particles_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html_ad1f02306798f50c9cbce664ea7c02105"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ad1f02306798f50c9cbce664ea7c02105">SPH::RelaxationOfAllDiffusionSpeciesRK2::exec</a></div><div class="ttdeci">virtual void exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.hpp:241</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_material_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a></div></div>
<div class="ttc" id="class_vecd_html"><div class="ttname"><a href="class_vecd.html">Vecd</a></div></div>
<div class="ttc" id="particle__dynamics__diffusion__reaction_8h_html"><div class="ttname"><a href="particle__dynamics__diffusion__reaction_8h.html">particle_dynamics_diffusion_reaction.h</a></div><div class="ttdoc">This is the particle dynamics applicable for all type bodies TODO: there is an issue on applying corr...</div></div>
<div class="ttc" id="namespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> solid_body_supplementary.cpp:9</div></div>
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